I think the main reason the Windows team generally discourages apps from including search boxes though is because they're afraid users won't learn to use the Search charm otherwise - i.e. if some apps start including search boxes, that will become the standard method of searching and all apps will "have to" include them, meaning a little more clutter for everyone. OTOH if all apps "hold the line" and rely on the Search charm instead, everyone will get accustomed to the Search charm method and every app's canvas / app bar gets a little more space and a little less clutter, plus a little more consistency. That's the idea anyway.
Perhaps they're trying to avoid this: